Most studies that have been conducted thus far with human genetic variation have been focused on single nucleotide polymorphisms (SNPs). These single base changes are relatively common in human populations, and almost 12 million SNPs have been identified at sites throughout the human genome. However, SNPs represent only a fraction of the genetic variation that exists in humans. Alternative forms of genetic variation, such as insertions and deletions (INDELs) and transposon insertions also are abundant in humans, yet these forms of genetic variation remain relatively unexplored. We have developed new experimental approaches to identify and study these alternative forms of genetic variation. We envision that integrated maps of natural genetic variation that include SNPs, INDELs, and transposon insertions will be more useful than SNP maps alone for identifying polymorphisms that directly influence human traits and diseases. Our future goals with this competitive renewal are to: (Aim 1) construct a comprehensive map of insertion and deletion (INDEL) variation in the human genome, (Aim 2) study INDEL patterns in human populations and (Aim 3) study INDEL variation that is caused by transposable genetic elements. These studies will immediately expand our knowledge of natural genetic variation in humans. Our long-term goal is to integrate these alternative forms of variation into the human HapMap and to study the impact of these variants on human phenotypes and diseases.